There are many options for the detection and speciation of microsporidia in clinical specimens. Light microscopy allows for detection of the parasites, but does not allow speciation. Electron microscopy is the gold standard for speciation, but is insensitive as a method for the detection of microsporidia. The polymerase chain reaction (PCR) is a sensitive technique with many different methods for confirming a positive result and determining the genus and species causing an infection. Speciation can be achieved by using species-specific primers in the PCR assay, or by using DNA probes or restriction endonucleases to determine the species after the PCR assay is performed. Single-strand conformation polymorphism (SSCP) analysis combined with PCR (PCR-SSCP) has been used to identify bacteria, fungi, and viruses. We will use our PCR assay to detect microsporidia in stool specimens and apply SSCP analysis to determine the genus and species of the parasite. Organisms from cell culture will also be used to validate the method.